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I sent you an email. Thank you so much for replying! I am very excited to try the C version.
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Originally posted by genericforms View PostI'm having a similar problem. I tried 4G, my average coverage is 30X and it dies whether I provide a region list or not. Any ideas? Did you guys figure out the problem above?
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I'm having a similar problem. I tried 4G, my average coverage is 30X and it dies whether I provide a region list or not. Any ideas? Did you guys figure out the problem above?
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Originally posted by seq_GA View PostHi
I tried using 10G without using any RANGE file (as it gives me different kind of problem), after a while smra crashes...
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I think you should mail the author your version number, STDERR report, etc.
What would happen if you tried it with
1) only chr1 ranges ?
2) only chr10 ranges ?
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Originally posted by nilshomer View PostYou don't need to adjust the heap size of SRMA, though add more memory with java ("java -Xmx2G -jar srma-0.1.6.jar"). The ranges must be in sorted order. Check the line at which it complains.
I tried using 10G without using any RANGE file (as it gives me different kind of problem), after a while smra crashes...
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Hi Zee,
I tried that also.
Its always breaking down when there is a trend in change of nimbers as below: When the nums change from 9 digit number to 5 digit number..
Code:chr1 247118921 247119161 chr1 247174632 247174752 [B]chr1 247177404 247179204 chr10 82880 83000[/B] chr10 83041 84088 chr10 84549 84669
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I think you should change your sort to
sort -k 1,1 -k 2n,2 range.txt -o range.txt
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Hi,
Thx for the suggestion. I tried using java -Xmx2G -jar and it crashed again. Now I am trying with 10G. Let me see whether it gets completed
Regarding my range file, its line 272 is as in the bold line. And it is tab delimited data.
chr10 102296881 102297001
chr10 102297801 102297921
chr10 1024383 1024503
chr10 102495968 102496088
chr10 102499456 102499696
I sorted my region of interest assort range.txt > range_sorted.txt
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Originally posted by seq_GA View PostHi,
The mean coverage is about 110. I am yet to try the heap size adn ranges file which is giving trouble.
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Hi,
The mean coverage is about 110. I am yet to try the heap size adn ranges file which is giving trouble.
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Originally posted by seq_GA View PostHow much should I specify for MAX_HEAP_SIZE?Originally posted by zee View PostI usually set my java memory heap quite high for this task e.g.
That gives it about 4Gb of RAM to work with. Perhaps bump yours up to 4/8Gb.
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I usually set my java memory heap quite high for this task e.g.
#!/bin/sh
# filename = srma & is executable
java -Xmx4000m -jar /export/opt/srma/build/jar/srma-0.1.6.jar $*
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smra error
Hi,
I am getting the following error while using smra.
Code:java -jar /srma/srma-0.1.6/srma-0.1.6.jar I=KLM_sorted.bam O=KLM_sorted_smra.bam R=/Genome/hg18/hg18.fa VALIDATION_STRINGEN CY=SILENT [Thu Jun 24 16:12:12 SGT 2010] srma.SRMA INPUT=KLM_sorted.bam OUTPUT=KLM_sorted_smra.bam REFERENCE=/Genome/hg18/hg18.fa VALIDATION_STRINGENCY=SILENT OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 NUM_THREADS=1 TMP_DIR=/tmp/userrig VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 Allele coverage cutoffs: coverage: 1 minimum allele coverage: 0 coverage: 2 minimum allele coverage: 0 coverage: 3 minimum allele coverage: 0 coverage: 4 minimum allele coverage: 1 coverage: 5 minimum allele coverage: 1 coverage: 6 minimum allele coverage: 1 coverage: 7 minimum allele coverage: 2 coverage: 8 minimum allele coverage: 2 coverage: 9 minimum allele coverage: 3 coverage: >9 minimum allele coverage: 3 Records processsed: 65534 (last chr10:1904158-1904236) Exception in thread "Thread-2" java.lang.OutOfMemoryError: Java heap space [Thu Jun 24 16:16:07 SGT 2010] srma.SRMA done. Runtime.totalMemory()=954466304 Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.LinkedList.addBefore(LinkedList.java:795) at java.util.LinkedList.add(LinkedList.java:215) at srma.ThreadPoolLinkedList.add(ThreadPoolLinkedList.java:19) at srma.SRMA.processToAddToGraphList(SRMA.java:485) at srma.SRMA.doWork(SRMA.java:272) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150) at srma.SRMA.main(SRMA.java:94)
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